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In order to run my microbial community samples from my experiments through DGGE, I was required to use multiple gels.

Thus it is necessary to compare banding patterns across more than one gel. This means that I need some way of assessing whether the 4th band on gel #1 is the same OTU as the 4th band on gel #2.

The industry standard for this procedure seems to be the Gelcompar software. Unfortunately this software is greater than $10,000 and is proprietary (thus, not open science friendly).

Does there exist a free (ideally as in speech and beer) alternative to Gelcompar?

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Do you have any programming skills? Because ImageJ immediately comes to mind. You'd just have to modify a little the already existing gel tools... – nico Jun 12 '12 at 5:17
I second the ImageJ recommendation. It's already well setup for gel analysis, and people do use it for DGGE (e.g…) – Richard Smith-Unna Jun 12 '12 at 10:42
Here's an ImageJ mailing list entry about DGGE... – Richard Smith-Unna Jun 12 '12 at 10:43
Phoretix 1D Pro is a cheaper alternative and yealy licenses are available – user4452 Sep 12 '13 at 14:26

Try this one

Pavel, A. B. & Vasile, C. I. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics 13, 9+ (2012).

You can download here

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